4Q1E
Human dCK C4S-S74E mutant in complex with UDP and the inhibitor 10 {2-{[(1R/S)-1-{2-[3-(2-fluoroethoxy)-4-methoxyphenyl]-5-methyl-1,3-thiazol 4-yl}ethyl]sulfanyl}pyrimidine-4,6-diamine}
X-RAY DIFFRACTION
Starting Model(s)
| Initial Refinement Model(s) | |||
|---|---|---|---|
| Type | Source | Accession Code | Details |
| experimental model | PDB | 4JLN | PDB entry 4JLN |
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION, HANGING DROP | 7.5 | 285 | 1.5 M trisodium citrate dehydrate and 25 mM HEPES pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 285K |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 2.21 | 44.27 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( ? ) | Angle ( ? ) |
| a = 68.736 | ¦Á = 90 |
| b = 68.736 | ¦Â = 90 |
| c = 122.206 | ¦Ã = 90 |
| Symmetry | |
|---|---|
| Space Group | P 41 |
Diffraction
| Diffraction Experiment | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
| 1 | 1 | x-ray | 93 | IMAGE PLATE | RIGAKU RAXIS IV++ | 2013-05-28 | M | SINGLE WAVELENGTH | ||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | ROTATING ANODE | RIGAKU RU200 | 1.5418 | ||
Data Collection
| Overall | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Sym I (Observed) | Net I Over Average Sigma (I) | Redundancy | Number Reflections (All) | Number Reflections (Observed) | Observed Criterion Sigma (F) | Observed Criterion Sigma (I) | B (Isotropic) From Wilson Plot | ||||||||
| 1 | 1.85 | 30 | 96.9 | 0.028 | 21.62 | 46762 | 46762 | ||||||||||||
| Highest Resolution Shell | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R-Sym I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
| 1 | 1.85 | 1.96 | 82.8 | 0.404 | 1.99 | 6415 | |||||||||||||
Refinement
| Statistics | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Number Reflections (All) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (All) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | ||||
| X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | PDB entry 4JLN | 1.85 | 27.92 | 43747 | 43747 | 2273 | 95.37 | 0.17609 | 0.17609 | 0.17399 | 0.21765 | RANDOM | 38.281 | ||||
| Temperature Factor Modeling | ||||||
|---|---|---|---|---|---|---|
| Anisotropic B[1][1] | Anisotropic B[1][2] | Anisotropic B[1][3] | Anisotropic B[2][2] | Anisotropic B[2][3] | Anisotropic B[3][3] | |
| -6.71 | -6.71 | 13.43 | ||||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 41.675 |
| r_dihedral_angle_4_deg | 18.363 |
| r_dihedral_angle_3_deg | 16.7 |
| r_dihedral_angle_1_deg | 6.131 |
| r_long_range_B_refined | 5.4 |
| r_long_range_B_other | 5.352 |
| r_scangle_other | 3.54 |
| r_mcangle_it | 3.4 |
| r_mcangle_other | 3.4 |
| r_mcbond_it | 2.497 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 3785 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 185 |
| Heterogen Atoms | 166 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| CrystalClear | data collection |
| MOLREP | phasing |
| REFMAC | refinement |
| XDS | data reduction |
| XDS | data scaling |
